A recent paper in the journal BIO-Complexity, authored by Winston Ewert, uses a dependency graph approach to model the relationships between the species. This idea is inspired by computer science which makes great use of dependency graphs for packaging of software and optimization of software architecture.

Complicated software applications typically use a wealth of lower level software routines. These routines have been developed, tested, and stored in modules for use by higher level applications. When this happens the application inherits the lower-level software and has a dependency on those modules.

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What Ewert has developed is a model to explain the pattern of similarities in different organisms that mimics how computer applications inherit software from a diverse range of lower-level modules. More.

a 2005 tree of life that includes horizontal gene transfer (HGT)/Andrew Z. Colvin, Barth F. Smets, with permission